TRACTOR db

Database Description

Experimental data on the Escherichia coli transcriptional regulatory system has been used in the past years to predict new regulatory elements (promoters, Transcription Factors (TFs), TFs' binding sites, operons) within its genome. As more genomes of gamma-proteobacteria are being sequenced, the prediction of these elements in a growing number of organisms has become more feasible, as a step towards the study of how different bacteria respond to environmental changes at the level of transcriptional regulation. In this work we present TRACTOR_DB (TRAnscription FaCTORsÿ predicted sites in prokaryotic genomes), a relational database that contains computational predictions of new members of 74 regulons in eight gamma-proteobacterial genomes. To produce these predictions we used a comparative genomics approach of which several proof-of-principle articles for large regulons have been published. Furthermore, we used the predictions stored in our database to assess the conservation of regulons' size across all the eight genomes and showed that a correlation exists between the conservation of a regulatory site and the structure of the Transcription Unit (TU) it regulates. TRACTOR_DB may be currently accessed at http://www.bioinfo.cu/database, http://www.tractor.lncc.br or at http://www.cifn.unam.mx/Computational_Genomics/.